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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggctgattgaaacccctctagttaatatatagaatgtgattgtaaacttctgagctcatgctaatacttgctgtggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG

Basic information

species Oryza sativa
transcript LOC_Os03g60740.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g60740.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G068244_T01 (Zea mays), 3'ss of exon 2
gttggctgattgaaacccctctagttaatata--------tagaatgtgattgtaaacttctgagctcatgctaatacttgctgtggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
|| || ||||          | || |  |||         | |||| || |  |  ||   | || |  || ||| | | | ||||||   ||||||||||||| ||||||||||||||||||| ||  |||
gtgggttgatgagtcttgtccaagcttgtatgccaattagtcgaatttgttattggacagtttagtttgtgataacattggttgtggttgtttagGTGGATTGGGTTGGCCAAAAGAATCAGATCGATGCTG

upper sequence: LOC_Os03g60740.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ29885 (Selaginella moellendorffii), 3'ss of exon 1
gttggctgattgaaacccctctagttaatatatagaatgtgattgtaaacttctgagctcatgctaatacttgctgtggtctgtt-agGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
                         | |     |   |    || |   | | ||| |||       |  || ||    | | |  ||||||||||||||||||| |||||||| |||||  |||
----------------------gtatgacggtcattctccttttctctgcctgtgatctctcatctcttttttctccattgtctccagGTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88573949|gb|CI665718.1|CI665718
EST:     AAGGTGGGAGGGCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGCCAAAGCTG
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGCCAAAGCTG
EST: gi|33818132|gb|CF334892.1|CF334892
EST:     AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagG-TGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|33818134|gb|CF334893.1|CF334893
EST:     AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|3762111|gb|C99359.1|C99359
EST:     AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|33686688|gb|CF314927.1|CF314927
EST:     AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|32947908|gb|BP184480.1|BP184480
EST:     AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|3762112|gb|C99360.1|C99360
EST:     AGTTTTACTATGAAGATGGAATGTANCCTGACCAG                         GTGGATTGGATTGCCCAAAAGAATCAGATTGACACTG
genomic: AGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|88395066|gb|CI609382.1|CI609382
EST:     AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTGGATTGGTCAAAAGAATCAGATTGACACTG
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|88308413|gb|CI650822.1|CI650822
EST:     AAGGTGGGAGGCCTGAGTTTCACTATGAAGATGGAATGTATCCTGAGCAC                         GTGGATTGGATTGGCCAAAAGAATCACATNGACACT
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACT
EST: gi|33817947|gb|CF334802.1|CF334802
EST:     ATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
genomic: ATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|117234788|gb|CT847886.1|CT847886
EST:     AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|33821837|gb|CF336729.1|CF336729
EST:     GGGTGGGAGGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTTGGATTGGCCAAAAGAATCAGATTGACACTG
genomic: GG-TGGGAGG-CCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATT-GGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|33817945|gb|CF334801.1|CF334801
EST:     AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|42592251|gb|CK738737.1|CK738737
EST:     AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
genomic: AAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
EST: gi|88576382|gb|CI670527.1|CI670527
EST:     GGTGGGAGGCCCTGAGTTTTACTATGAAGATGGAATGTANTC-TGAGCAG                         GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGCCAAAGCTG
genomic: GGTGGGAGGCC-TGAGTTTTACTATGAAGATGGAATGTA-TCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGCCAAAGCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 62 (downstream exon)
Score: 70

AATCCTCACGAGTGCTGTGCCAAAGATGAAACCTGGTTTTGACCCTAGCAAAGGTGGGAGGCCTGAGTTTTACTATGAAGATGGAATGTATCCTGAGCAGgttggctgat ... ggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaatgtgattgtaaacttctgagctcatgctaatacttgctgtggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG
                             tgctaat  putative branch site (score: 70)
         attgtaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggctgattgaaacccctctagttaatatatagaatgtgattgtaaacttctgagctcatgctaatacttgctgtggtctgttagGTGGATTGGATTGGCCAAAAGAATCAGATTGACACTG

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